1. TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations 
Jason A. O’Rawe, Yiyang Wu, Max J. Dörfel, Alan F. Rope, P.Y. Billie Au, Jillian S. Parboosingh, Sungjin Moon, Maria Kousi, Konstantina Kosma, Christopher S. Smith, Maria Tzetis, Jane L. Schuette, Robert B. Hufnagel, Carlos E. Prada, Francisco Martinez, Carmen Orellana, Jonathan Crain, Alfonso Caro-Llopis, Silvestre Oltra, Sandra Monfort, Laura T. Jiménez-Barrón, Jeffrey Swensen, Sara Ellingwood, Rosemarie Smith, Han Fang, Sandra Ospina, Sander Stegmann, Nicolette Den Hollander, David Mittelman, Gareth Highnam, Reid Robison, Edward Yang, Laurence Faivre, Agathe Roubertie, Jean-Baptiste Rivière, Kristin G. Monaghan, Kai Wang, Erica E. Davis, Nicholas Katsanis, Vera M. Kalscheuer, Edith H. Wang, Kay Metcalfe, Tjitske Kleefstra, A. Micheil Innes, Sophia Kitsiou- Tzeli, Monica Rosello, Catherine E. Keegan, Gholson J. Lyon 
The American Journal of Human Genetics 
Volume 97, Issue 6, Pages (December 2015)
DOI: /j.ajhg
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2. Figure 1 Images of the Facial Phenotype from Families 1, 2, and 4–9
Cardinal facial dysmorphologies include prominent supraorbital ridges (seen in 1A, 1B, 2A, 6A, 8A–8C, and 9A), down-slanted palpebral fissures (1A, 1B, 2A, 4A, 5A, 6A, 8A–8C, and 9A), sagging cheeks (1A, 1B, 5A, 8A–8C, and 9A), a long philtrum (1A, 1B, 2A, 4A, 5A, 8A–8C, and 9A), low-set and protruding ears (1A, 1B, 2A, 4A, 5A, 6A, 8A–8C, and 9A), a long face (1A, 1B, 2A, 5A, 6A, 8A–8C, and 9A), a high palate (5A, 6A, 8A–8C, and 9A), a pointed chin (1A, 1B, 2A, 4A, 5A, 6A, and 8A–8C), and anteverted nares (2A, 4A, 5A, 7A, 8A–8C, and 9A).
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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3. Figure 2
TAF1 Domains, Variant Scores, and ExAC Sequence Variation Plot
(A) Pedigree drawings of the nine families who were found to harbor TAF1 SNVs (NCBI Gene ID: 6872 according to the GRCh37.p13 assembly). Black dots indicate maternal carriers.
(B) All nine SNVs are listed and annotated with CADD, SIFT, GERP++, and phyloP scores (which indicate conservation across 99 vertebrate genomes and humans). All of the SNVs are considered to be potentially deleterious by all of the listed annotations, except for c.3708A>G, which is a splice-site variant and as a consequence is not necessarily expected to be categorized as deleterious by any of the listed scores, because it does not affect amino acid composition of the predicted protein.
(C) Known TAF1 domains are shown with respect to their corresponding genic positions. All but non-synonymous variants reported in the ExAC Browser for TAF1 are plotted below as lines; white and gray indicate exon boundaries. Red lines indicate the relative positions of the eight missense variants described in this paper (see Table 2). Numerals link the sequence variants shown on the ExAC plot to their familial origin, and those noted with a star fall within TAF1 regions that are significantly underrepresented by non-synonymous sequence variation in the ExAC Browser in European and Latin populations (p values of and for the first [c.2419T>C, c.2926G>C, and c.3736C>T] and second [c.3708A>G ] clusters, according to Cucala’s hypothesis-free multiple scan statistic with a variable window27).
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4. Figure 3 Duplications Involving TAF1 from Families 10 and 11
(A) Pedigree drawings of families 10 and 11.
(B) The facial phenotype of proband 10A is notable for prominent supraorbital ridges, down-slanted palpebral fissures, sagging cheeks, a long face, a high palate, and a pointed chin.
(C) Chromosome X cytobands are plotted above a more focused view of the region containing duplications that involve TAF1 in families 10 and 11. UCSC refGenes (from the UCSC Genome Browser tables) whose canonical transcript start or stop sites overlap either of the two duplications are plotted.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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5. Figure 4
Suppression or Genetic Mutation of Endogenous taf1 Induces Decreased Size of the Optic Tectum In Vivo
(A) Dorsal view of a control embryo (top) and an embryo injected with a morpholino (MO) targeting the donor site of exon 9 of D. rerio taf1 3 days after fertilization. An antibody against α-acetylated tubulin was used for visualizing the axon tracts in the brain of evaluated embryos. The assay consisted of measuring the area of the optic tectum (highlighted with the dashed ellipse), a neuroanatomical structure that occupies the majority of the space within the midbrain.
(B) A boxplot shows quantitative differences in the size of the optic tectum for each condition tested across three biological replicates. Suppression of taf1 consistently induced a decrease of ∼10% in the relative area of the optic tectum (p < ). The MO phenotype could be restored by co-injection of MO and wild-type (WT) human TAF1 mRNA (p < ), denoting the specificity of the phenotype due to taf1 suppression. Overexpression of WT human TAF1 mRNA alone did not induce a phenotype that was significantly different from that of controls (p = 0.79). The numbers of embryos evaluated per condition were as follows: control, 134; taf1 MO, 133; taf1 MO + WT TAF1 RNA, 109; and WT TAF1 RNA, 78.
(C) A boxplot shows quantitative differences in the size of the optic tectum between uninjected controls and F0 embryos with CRISPR-disrupted taf1. The phenotype observed for both MO-injected embryos and embryos with CRISPR-disrupted taf1 was concordant and reproducible across different experiments and across the two different methodologies. The p values were calculated with a Student’s t test.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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